rs4078417

Variant names:

• chr14-51290164-A-C
• rs4078417
• XR_007064164.1:n.633+2101A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007064164.1(LOC124903315):​n.633+2101A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,164 control chromosomes in the GnomAD database, including 6,356 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.25 (6356 hom., cov: 32)
• Consequence: LOC124903315 XR_007064164.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.774
• Publications: 3 publications found

Genes affected

LOC124903315 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903315	XR_007064164.1	n.633+2101A>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38530 AN: 152046 Hom.: 6352 Cov.: 32

Gnomad AFR AF: 0.0642

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.0399

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.257

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.253 AC: 38540 AN: 152164 Hom.: 6356 Cov.: 32 AF XY: 0.251 AC XY: 18694 AN XY: 74384

African (AFR) AF: 0.0640 AC: 2659 AN: 41550

American (AMR) AF: 0.327 AC: 5003 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 993 AN: 3470

East Asian (EAS) AF: 0.0402 AC: 208 AN: 5178

South Asian (SAS) AF: 0.223 AC: 1077 AN: 4822

European-Finnish (FIN) AF: 0.316 AC: 3344 AN: 10574

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24282 AN: 67974

Other (OTH) AF: 0.254 AC: 536 AN: 2114

Alfa AF: 0.315 Hom.: 16419

Bravo AF: 0.248

Asia WGS AF: 0.160 AC: 554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.45
PhyloP100		0.77

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4078417; hg19: chr14-51756882;